@article{Georg:2018,
  author = {Steffen C. Lott and Richard A Sch{\"a}fer and Martin Mann and Rolf Backofen and Wolfgang R Hess and Bj{\"o}rn Voss and Jens Georg},
  title = {{GLASSgo} - Automated and reliable detection of {sRNA} homologs from a single input sequences},
  journal = {Frontiers in Genetics},
issn = {1664-8021},
  volume = {9},
  number = {},
  pages = {124},
  year = {2018},
  doi = {10.3389/fgene.2018.00124},
user = {mmann},
abstract = {Bacterial small RNAs (sRNAs) are important post-transcriptional regulators of 
gene expression. The functional and evolutionary characterization of sRNAs 
requires the identification of homologs, which is frequently challenging due 
to their heterogeneity, short length and partly, little sequence conservation. 
We developed the GLobal Automatic Small RNA Search go (GLASSgo) algorithm to 
identify sRNA homologs in complex genomic databases starting from a single 
sequence. GLASSgo combines an iterative BLAST strategy with pairwise identity 
filtering and a graph-based clustering method that utilizes RNA secondary 
structure information. We tested the specificity, sensitivity and runtime of 
GLASSgo, BLAST and the combination RNAlien/cmsearch in a typical use case 
scenario on 40 bacterial sRNA families. The sensitivity of the tested methods 
was similar, while the specificity of GLASSgo and RNAlien/cmsearch was 
significantly higher than that of BLAST. GLASSgo was on average about 87 times 
faster than RNAlien/cmsearch, and only about 7.5 times slower than BLAST, 
which shows that GLASSgo optimizes the trade-off between speed and accuracy in 
the task of finding sRNA homologs. GLASSgo is fully automated, whereas BLAST 
often recovers only parts of homologs and RNAlien/cmsearch requires extensive 
additional bioinformatic work to get a comprehensive set of homologs. GLASSgo 
is available as an easy-to-use web server to find homologous sRNAs in large 
databases.}
}